[gmx-users] lincs errors late in simulation

Justin Lemkul jalemkul at vt.edu
Tue May 14 18:09:44 CEST 2013

On 5/14/13 10:27 AM, Joe Smerdon wrote:
> Hi all,
> First of all I'm new to md simulations, so if I am missing anything simple, I would be grateful for any pointers, however small.  I am trying to simulate many small molecules on a substrate.  I am restraining my substrate from moving but allowing the molecules to do whatever they like.  My steps are to minimise my system (136 molecules on a 200Ax200A surface of about 4 layers, with 100A vacuum), then to run an NVT simulation without pbcs (though I could use pbcs, I just don't really need to for this).  I am getting LINCS errors late on in the simulations - they don't always cause a crash, but sometimes they do.  I guess it can't be insufficient minimisation if the errors arise after the simulation has been underway for awhile (eg, step 15000, 8ps into a 50ps simulation), but I don't really know what it can be.  My timestep is 0.5 fs.  I am just experimenting at the moment, I intend to simulate for much longer when I get it working.
> I guess my question is: are LINCS errors that occur late in a simulation due to poor minimisation, or not?  If not, what other factors should I look at?

Failures at 8 ps are not considered late.  There are a whole host of problems 
that could be present, ranging from .mdp settings to topologies.  See standard 
advice for diagnosing at 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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